ENST00000569074.1:n.216-12994C>A

Variant names:

• chr17-71112612-G-T
• rs1859962
• ENST00000569074.1:n.216-12994C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000569074.1(CASC17):​n.216-12994C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,984 control chromosomes in the GnomAD database, including 24,465 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24465 hom., cov: 32)
• Consequence: CASC17 ENST00000569074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 169 publications found

Genes affected

CASC17 (HGNC:43911): (cancer susceptibility 17)

ENSG00000300867 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000569074.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	NR_104152.1		n.218-12994C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CASC17	ENST00000569074.1	TSL:1	n.216-12994C>A		intron	N/A
	CASC17	ENST00000659322.1		n.556-12994C>A		intron	N/A
	CASC17	ENST00000659670.1		n.252-12994C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85073 AN: 151866 Hom.: 24444 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.511

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.560 AC: 85130 AN: 151984 Hom.: 24465 Cov.: 32 AF XY: 0.556 AC XY: 41255 AN XY: 74258

African (AFR) AF: 0.693 AC: 28755 AN: 41474

American (AMR) AF: 0.464 AC: 7079 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1560 AN: 3472

East Asian (EAS) AF: 0.624 AC: 3223 AN: 5166

South Asian (SAS) AF: 0.448 AC: 2158 AN: 4820

European-Finnish (FIN) AF: 0.499 AC: 5254 AN: 10524

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35374 AN: 67948

Other (OTH) AF: 0.509 AC: 1073 AN: 2110

Alfa AF: 0.529 Hom.: 98075

Bravo AF: 0.565

Asia WGS AF: 0.572 AC: 1990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1859962; hg19: chr17-69108753;